Here's an analogy that I can speak from more direct experience: if you study the theory of elliptic curves, and then look at elliptic curve cryptography code, t

Here's an analogy that I can speak from more direct experience: if you study the theory of elliptic curves, and then look at elliptic curve cryptography code, there will appear to be no connection between the two. This is because in between the theory and the code are a zillion implementation details and tricks of the trade that aren't generally mentioned in the theory. Add to that the fact that the people who write scientific code aren't coders by trade, so they learn to write code that is just good enough but no better, and the result is something that looks like a horrible mess. (Also, the code is often written by grad students, so that makes it even worse. I look back on some of the code that I wrote back when I was a grad student that was the basis for publications and I shudder.)